earlyR: Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

Version: 0.0.1
Depends: R (≥ 3.3.0)
Imports: stats, distcrete, EpiEstim, epitrix
Suggests: testthat, vdiffr, roxygen2, incidence, knitr
Published: 2017-12-06
Author: Thibaut Jombart [aut, cre], Anne Cori [aut], Pierre Nouvellet [aut]
Maintainer: Thibaut Jombart <thibautjombart at gmail.com>
BugReports: https://github.com/reconhub/earlyR/issues
License: MIT + file LICENSE
URL: http://www.repidemicsconsortium.org/earlyR
NeedsCompilation: no
Materials: NEWS
CRAN checks: earlyR results

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Reference manual: earlyR.pdf
Package source: earlyR_0.0.1.tar.gz
Windows binaries: r-devel: earlyR_0.0.1.zip, r-release: earlyR_0.0.1.zip, r-oldrel: earlyR_0.0.1.zip
OS X El Capitan binaries: r-release: earlyR_0.0.1.tgz
OS X Mavericks binaries: r-oldrel: earlyR_0.0.1.tgz

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